https://github.com/afrendeiro/pipelines/ is deprecated!

See https://github.com/epigen/open_pipelines/ for NGS pipelines and https://github.com/epigen/looper/ for a pipeline/job submission engine/manager

pipelines

Instalation

Clone the repository

git clone git@github.com:afrendeiro/pipelines.git
cd pipelines

Install module:

python setup.py install

or with pip:

pip install .

If not root, add the --user to either command to install to your home directory.

Dependencies will be installed as well if these are not met.

You'll have now a ngsProject command in your $PATH. Type ngsProject -h to see all options.

Additionally, you'll also have a .pipeline_config.yaml file in your $HOME upon installation.

Config file

The .pipeline_config.yaml in your $HOME contains configurations that are read by the pipeline objects.

A thorough description of the recognised configurations will soon follow.

Sample annotation sheet

The sample annotation sheet is a csv file containing sample annotation. It is passed as argument to ngsProject.

Columns recognized are: cellLine, numberCells, technique, ip, patient, patientID, sampleID, treatment, biologicalReplicate, technicalReplicate, experimentName, genome, unmappedBam, but others might be present as well.

Required fields are: technique, genome and unmappedBam